Starting phenix.real_space_refine on Wed Jun 18 07:26:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.map" model { file = "/net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lj2_63131/06_2025/9lj2_63131.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 298 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 12448 2.51 5 N 3821 2.21 5 O 4524 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21131 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3002 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3025 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 4921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4921 Classifications: {'peptide': 598} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Chain: "N" Number of atoms: 4066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4066 Classifications: {'peptide': 495} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 477} Chain breaks: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.59, per 1000 atoms: 0.60 Number of scatterers: 21131 At special positions: 0 Unit cell: (114.745, 117.992, 194.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 38 16.00 P 298 15.00 Mg 2 11.99 O 4524 8.00 N 3821 7.00 C 12448 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.2 seconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 60.6% alpha, 4.1% beta 137 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 9.00 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 86 through 114 removed outlier: 3.533A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.741A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.249A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.584A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.598A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.548A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.652A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.016A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.780A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.562A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 76 Processing helix chain 'K' and resid 82 through 90 removed outlier: 4.049A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 129 removed outlier: 3.705A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER K 125 " --> pdb=" O HIS K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 143 removed outlier: 3.654A pdb=" N ARG K 134 " --> pdb=" O ASP K 130 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 302 through 309 removed outlier: 3.867A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 315 removed outlier: 3.676A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 4.037A pdb=" N ARG K 328 " --> pdb=" O GLU K 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 340 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.935A pdb=" N LEU K 370 " --> pdb=" O LEU K 366 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.829A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 392 through 397 Processing helix chain 'K' and resid 405 through 409 removed outlier: 4.050A pdb=" N LEU K 409 " --> pdb=" O GLN K 406 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 417 removed outlier: 3.880A pdb=" N VAL K 417 " --> pdb=" O LYS K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 467 through 478 removed outlier: 3.639A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 497 through 500 removed outlier: 3.578A pdb=" N ASN K 500 " --> pdb=" O LEU K 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 497 through 500' Processing helix chain 'K' and resid 501 through 518 Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.693A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 609 removed outlier: 3.777A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 609 through 614 removed outlier: 3.778A pdb=" N HIS K 613 " --> pdb=" O MET K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.795A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.701A pdb=" N LEU K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 730 through 735 Processing helix chain 'N' and resid 102 through 115 removed outlier: 3.648A pdb=" N PHE N 109 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU N 110 " --> pdb=" O THR N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 126 Processing helix chain 'N' and resid 133 through 139 removed outlier: 3.731A pdb=" N VAL N 139 " --> pdb=" O GLN N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 143 Processing helix chain 'N' and resid 197 through 214 removed outlier: 3.850A pdb=" N ILE N 201 " --> pdb=" O ARG N 197 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN N 202 " --> pdb=" O PRO N 198 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY N 203 " --> pdb=" O TYR N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 241 removed outlier: 4.095A pdb=" N PHE N 234 " --> pdb=" O GLN N 230 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU N 235 " --> pdb=" O THR N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 255 No H-bonds generated for 'chain 'N' and resid 253 through 255' Processing helix chain 'N' and resid 256 through 268 removed outlier: 3.650A pdb=" N TRP N 260 " --> pdb=" O THR N 256 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU N 261 " --> pdb=" O LEU N 257 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG N 266 " --> pdb=" O ARG N 262 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) Processing helix chain 'N' and resid 279 through 290 removed outlier: 3.545A pdb=" N ARG N 283 " --> pdb=" O ASP N 279 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA N 284 " --> pdb=" O LYS N 280 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 302 through 307 removed outlier: 3.618A pdb=" N ILE N 307 " --> pdb=" O TYR N 303 " (cutoff:3.500A) Processing helix chain 'N' and resid 309 through 316 removed outlier: 3.567A pdb=" N LEU N 313 " --> pdb=" O GLU N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 326 through 329 Processing helix chain 'N' and resid 334 through 341 removed outlier: 3.518A pdb=" N ARG N 341 " --> pdb=" O SER N 337 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 371 removed outlier: 3.769A pdb=" N TRP N 364 " --> pdb=" O LEU N 360 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA N 365 " --> pdb=" O HIS N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 391 removed outlier: 3.859A pdb=" N THR N 390 " --> pdb=" O SER N 386 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU N 391 " --> pdb=" O SER N 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 396 through 405 removed outlier: 3.695A pdb=" N THR N 403 " --> pdb=" O LYS N 399 " (cutoff:3.500A) Processing helix chain 'N' and resid 434 through 446 Processing helix chain 'N' and resid 467 through 478 Processing helix chain 'N' and resid 479 through 483 removed outlier: 3.695A pdb=" N ASP N 483 " --> pdb=" O TYR N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 500 removed outlier: 4.060A pdb=" N VAL N 498 " --> pdb=" O ASP N 494 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN N 500 " --> pdb=" O HIS N 496 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 516 removed outlier: 3.647A pdb=" N LYS N 509 " --> pdb=" O GLN N 505 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS N 515 " --> pdb=" O LEU N 511 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 541 removed outlier: 3.594A pdb=" N ASP N 532 " --> pdb=" O SER N 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE N 533 " --> pdb=" O ARG N 529 " (cutoff:3.500A) Processing helix chain 'N' and resid 553 through 565 Processing helix chain 'N' and resid 601 through 613 removed outlier: 3.507A pdb=" N ASP N 605 " --> pdb=" O ASN N 601 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA N 608 " --> pdb=" O ALA N 604 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA N 612 " --> pdb=" O ALA N 608 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 651 removed outlier: 4.199A pdb=" N LYS N 635 " --> pdb=" O SER N 631 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU N 638 " --> pdb=" O GLU N 634 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP N 647 " --> pdb=" O LYS N 643 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN N 648 " --> pdb=" O LEU N 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.518A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.629A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.040A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.861A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 248 through 251 removed outlier: 5.973A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 273 through 275 Processing sheet with id=AB3, first strand: chain 'K' and resid 429 through 431 removed outlier: 6.953A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N LEU K 576 " --> pdb=" O VAL K 521 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE K 523 " --> pdb=" O LEU K 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 320 through 324 removed outlier: 6.030A pdb=" N ILE N 321 " --> pdb=" O LEU N 349 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE N 351 " --> pdb=" O ILE N 321 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE N 323 " --> pdb=" O ILE N 351 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY N 217 " --> pdb=" O ARG N 348 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU N 350 " --> pdb=" O GLY N 217 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE N 218 " --> pdb=" O LEU N 410 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 425 through 426 removed outlier: 6.325A pdb=" N LYS N 425 " --> pdb=" O VAL N 623 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ARG N 625 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL N 521 " --> pdb=" O PHE N 574 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU N 576 " --> pdb=" O VAL N 521 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE N 523 " --> pdb=" O LEU N 576 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N CYS N 546 " --> pdb=" O LEU N 575 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N THR N 577 " --> pdb=" O CYS N 546 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 430 through 431 731 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 672 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 10.23 Time building geometry restraints manager: 6.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4790 1.33 - 1.45: 5736 1.45 - 1.57: 10933 1.57 - 1.69: 593 1.69 - 1.81: 64 Bond restraints: 22116 Sorted by residual: bond pdb=" CA ASP N 483 " pdb=" C ASP N 483 " ideal model delta sigma weight residual 1.532 1.498 0.035 9.60e-03 1.09e+04 1.31e+01 bond pdb=" CB PRO N 567 " pdb=" CG PRO N 567 " ideal model delta sigma weight residual 1.492 1.668 -0.176 5.00e-02 4.00e+02 1.24e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" C PHE N 482 " pdb=" N ASP N 483 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.19e-02 7.06e+03 6.07e+00 bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.522 1.494 0.029 1.20e-02 6.94e+03 5.72e+00 ... (remaining 22111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 30775 2.61 - 5.22: 319 5.22 - 7.83: 31 7.83 - 10.44: 3 10.44 - 13.05: 1 Bond angle restraints: 31129 Sorted by residual: angle pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" CD PRO N 567 " ideal model delta sigma weight residual 112.00 98.95 13.05 1.40e+00 5.10e-01 8.69e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 114.62 108.50 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 108.46 4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" N PRO N 567 " pdb=" CD PRO N 567 " pdb=" CG PRO N 567 " ideal model delta sigma weight residual 103.20 96.53 6.67 1.50e+00 4.44e-01 1.98e+01 angle pdb=" N THR A 80 " pdb=" CA THR A 80 " pdb=" C THR A 80 " ideal model delta sigma weight residual 108.65 100.87 7.78 1.85e+00 2.92e-01 1.77e+01 ... (remaining 31124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 11134 35.33 - 70.66: 1473 70.66 - 105.99: 23 105.99 - 141.32: 16 141.32 - 176.65: 6 Dihedral angle restraints: 12652 sinusoidal: 7205 harmonic: 5447 Sorted by residual: dihedral pdb=" O2A ADP K1202 " pdb=" O3A ADP K1202 " pdb=" PA ADP K1202 " pdb=" PB ADP K1202 " ideal model delta sinusoidal sigma weight residual 300.00 123.35 176.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " pdb=" O2A ADP K1202 " ideal model delta sinusoidal sigma weight residual -60.00 83.29 -143.29 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" C4' ADP K1202 " pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " ideal model delta sinusoidal sigma weight residual -180.00 -71.47 -108.53 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 12649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2461 0.039 - 0.078: 808 0.078 - 0.116: 200 0.116 - 0.155: 34 0.155 - 0.194: 6 Chirality restraints: 3509 Sorted by residual: chirality pdb=" CA PRO N 567 " pdb=" N PRO N 567 " pdb=" C PRO N 567 " pdb=" CB PRO N 567 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CG LEU N 576 " pdb=" CB LEU N 576 " pdb=" CD1 LEU N 576 " pdb=" CD2 LEU N 576 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.64e-01 ... (remaining 3506 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA N 566 " 0.089 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO N 567 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO N 567 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO N 567 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA K 566 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO K 567 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO K 567 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 567 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 72 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.76e+00 pdb=" N PRO K 73 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO K 73 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 73 " -0.031 5.00e-02 4.00e+02 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 370 2.62 - 3.19: 18745 3.19 - 3.76: 36812 3.76 - 4.33: 49438 4.33 - 4.90: 73321 Nonbonded interactions: 178686 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 2.044 2.170 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.083 3.120 nonbonded pdb=" O2 DC I 92 " pdb=" N2 DG J 56 " model vdw 2.119 2.496 nonbonded pdb=" OG SER K 434 " pdb=" OE1 GLN K 437 " model vdw 2.120 3.040 nonbonded pdb="MG MG N1201 " pdb=" O3B ADP N1202 " model vdw 2.155 2.170 ... (remaining 178681 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 15 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid 1 through 55 or resid 57 through 64 or resid 67 or resid 6 \ 9 through 74 or resid 76 through 77 or resid 79 or resid 83 through 88 or resid \ 90 through 91 or resid 93 through 147)) selection = (chain 'J' and (resid 1 through 55 or resid 57 through 61 or resid 63 through 65 \ or resid 68 or resid 71 through 72 or resid 74 through 79 or resid 81 or resid \ 84 through 91 or resid 93 through 147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.420 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.176 22116 Z= 0.230 Angle : 0.732 13.049 31129 Z= 0.422 Chirality : 0.041 0.194 3509 Planarity : 0.005 0.124 2931 Dihedral : 24.540 176.649 9116 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.18 % Allowed : 0.49 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1825 helix: 0.80 (0.17), residues: 1001 sheet: -2.56 (0.51), residues: 103 loop : -1.96 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 260 HIS 0.005 0.001 HIS B 18 PHE 0.018 0.002 PHE K 574 TYR 0.015 0.002 TYR K 543 ARG 0.015 0.001 ARG C 42 Details of bonding type rmsd hydrogen bonds : bond 0.14049 ( 1073) hydrogen bonds : angle 5.30456 ( 2808) covalent geometry : bond 0.00512 (22116) covalent geometry : angle 0.73215 (31129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8126 (mm-30) REVERT: E 106 ASP cc_start: 0.7891 (m-30) cc_final: 0.7425 (m-30) REVERT: E 120 MET cc_start: 0.7563 (mtt) cc_final: 0.7217 (mtt) REVERT: G 104 GLN cc_start: 0.8512 (mm110) cc_final: 0.8281 (mm110) REVERT: H 90 GLU cc_start: 0.8250 (mp0) cc_final: 0.7835 (mp0) REVERT: K 183 PHE cc_start: 0.8833 (m-10) cc_final: 0.8311 (m-10) REVERT: K 722 LEU cc_start: 0.7881 (mm) cc_final: 0.7619 (mm) REVERT: N 645 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8913 (ttp80) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 1.5644 time to fit residues: 420.8536 Evaluate side-chains 162 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 122 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.5980 chunk 157 optimal weight: 0.0870 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 44 GLN G 104 GLN K 111 HIS ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS N 121 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.094061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067264 restraints weight = 62337.157| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.70 r_work: 0.3082 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22116 Z= 0.165 Angle : 0.669 8.500 31129 Z= 0.362 Chirality : 0.039 0.190 3509 Planarity : 0.005 0.056 2931 Dihedral : 28.545 171.874 5297 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.66 % Allowed : 10.26 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.21), residues: 1825 helix: 1.15 (0.17), residues: 1019 sheet: -2.31 (0.47), residues: 113 loop : -1.78 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 260 HIS 0.013 0.001 HIS K 361 PHE 0.014 0.002 PHE N 234 TYR 0.014 0.001 TYR K 543 ARG 0.004 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05568 ( 1073) hydrogen bonds : angle 4.13242 ( 2808) covalent geometry : bond 0.00361 (22116) covalent geometry : angle 0.66918 (31129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8594 (t0) cc_final: 0.8266 (t0) REVERT: D 33 SER cc_start: 0.8595 (t) cc_final: 0.8373 (t) REVERT: D 105 LYS cc_start: 0.8722 (mtpm) cc_final: 0.8470 (mttp) REVERT: E 73 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8678 (tm-30) REVERT: E 106 ASP cc_start: 0.8372 (m-30) cc_final: 0.8011 (m-30) REVERT: E 120 MET cc_start: 0.8198 (mtt) cc_final: 0.7863 (mtt) REVERT: F 93 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: G 104 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8742 (mm110) REVERT: H 39 TYR cc_start: 0.8705 (t80) cc_final: 0.8472 (t80) REVERT: H 53 SER cc_start: 0.9405 (t) cc_final: 0.9177 (p) REVERT: H 90 GLU cc_start: 0.8817 (mp0) cc_final: 0.8564 (mp0) REVERT: K 183 PHE cc_start: 0.8766 (m-10) cc_final: 0.8543 (m-10) REVERT: K 525 SER cc_start: 0.9159 (m) cc_final: 0.8513 (t) REVERT: K 722 LEU cc_start: 0.7722 (mm) cc_final: 0.7449 (mm) REVERT: N 279 ASP cc_start: 0.8625 (t0) cc_final: 0.8415 (t70) REVERT: N 606 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8195 (tm) REVERT: N 645 ARG cc_start: 0.8957 (ttp80) cc_final: 0.8719 (ttp80) outliers start: 27 outliers final: 7 residues processed: 218 average time/residue: 1.4586 time to fit residues: 358.4242 Evaluate side-chains 181 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 172 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 606 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 201 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 163 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 85 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 347 ASN K 361 HIS ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.091388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.063928 restraints weight = 61627.515| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.68 r_work: 0.2995 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 22116 Z= 0.310 Angle : 0.713 8.837 31129 Z= 0.387 Chirality : 0.042 0.166 3509 Planarity : 0.005 0.053 2931 Dihedral : 28.703 168.598 5295 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.52 % Allowed : 14.51 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1825 helix: 0.98 (0.16), residues: 1035 sheet: -2.24 (0.47), residues: 112 loop : -1.89 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 267 HIS 0.013 0.001 HIS K 361 PHE 0.024 0.002 PHE N 122 TYR 0.018 0.002 TYR N 499 ARG 0.008 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.06526 ( 1073) hydrogen bonds : angle 4.16109 ( 2808) covalent geometry : bond 0.00710 (22116) covalent geometry : angle 0.71340 (31129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8899 (tm) REVERT: C 90 ASP cc_start: 0.8636 (t0) cc_final: 0.8406 (t0) REVERT: D 105 LYS cc_start: 0.9014 (mtpm) cc_final: 0.8792 (mttp) REVERT: E 73 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8680 (tm-30) REVERT: E 106 ASP cc_start: 0.8446 (m-30) cc_final: 0.8097 (m-30) REVERT: E 120 MET cc_start: 0.8386 (mtt) cc_final: 0.8035 (mtt) REVERT: F 93 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: G 104 GLN cc_start: 0.9079 (mm-40) cc_final: 0.8818 (mm110) REVERT: H 39 TYR cc_start: 0.8788 (t80) cc_final: 0.8535 (t80) REVERT: H 90 GLU cc_start: 0.8884 (mp0) cc_final: 0.8480 (mp0) REVERT: K 424 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7663 (ttpt) REVERT: K 722 LEU cc_start: 0.7889 (mm) cc_final: 0.7641 (mm) REVERT: N 279 ASP cc_start: 0.8660 (t0) cc_final: 0.8450 (t70) outliers start: 41 outliers final: 18 residues processed: 196 average time/residue: 1.4167 time to fit residues: 313.3284 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 361 HIS Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 198 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** K 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS K 437 GLN ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN N 505 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066460 restraints weight = 62248.770| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.71 r_work: 0.3074 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22116 Z= 0.158 Angle : 0.636 10.490 31129 Z= 0.345 Chirality : 0.038 0.171 3509 Planarity : 0.004 0.054 2931 Dihedral : 28.461 166.348 5295 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.40 % Allowed : 16.78 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1825 helix: 1.24 (0.17), residues: 1037 sheet: -1.96 (0.46), residues: 123 loop : -1.74 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 260 HIS 0.013 0.001 HIS K 361 PHE 0.027 0.002 PHE N 122 TYR 0.019 0.001 TYR N 499 ARG 0.005 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.05173 ( 1073) hydrogen bonds : angle 3.82489 ( 2808) covalent geometry : bond 0.00347 (22116) covalent geometry : angle 0.63601 (31129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8781 (tm) REVERT: A 94 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8596 (mm-30) REVERT: C 90 ASP cc_start: 0.8507 (t0) cc_final: 0.8258 (t0) REVERT: D 33 SER cc_start: 0.8532 (t) cc_final: 0.8316 (t) REVERT: D 39 TYR cc_start: 0.8715 (t80) cc_final: 0.8227 (t80) REVERT: D 90 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: D 105 LYS cc_start: 0.8828 (mtpm) cc_final: 0.8596 (mttp) REVERT: E 68 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: E 73 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8670 (tm-30) REVERT: E 106 ASP cc_start: 0.8359 (m-30) cc_final: 0.8010 (m-30) REVERT: E 120 MET cc_start: 0.8181 (mtt) cc_final: 0.7789 (mtt) REVERT: F 93 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7037 (mp10) REVERT: G 104 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8731 (mm110) REVERT: H 53 SER cc_start: 0.9402 (t) cc_final: 0.9171 (p) REVERT: H 90 GLU cc_start: 0.8904 (mp0) cc_final: 0.8462 (mp0) REVERT: K 279 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7499 (p0) REVERT: K 722 LEU cc_start: 0.7811 (mm) cc_final: 0.7570 (mm) REVERT: N 221 ASP cc_start: 0.6630 (m-30) cc_final: 0.6383 (m-30) REVERT: N 469 MET cc_start: 0.8299 (tpp) cc_final: 0.8078 (tpp) REVERT: N 470 MET cc_start: 0.8359 (ttp) cc_final: 0.8050 (ttp) REVERT: N 606 LEU cc_start: 0.8666 (mt) cc_final: 0.8412 (tm) outliers start: 39 outliers final: 11 residues processed: 207 average time/residue: 1.4125 time to fit residues: 330.2939 Evaluate side-chains 176 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 370 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 112 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 179 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.094362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.067519 restraints weight = 62794.741| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.70 r_work: 0.3104 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22116 Z= 0.145 Angle : 0.627 12.694 31129 Z= 0.338 Chirality : 0.037 0.170 3509 Planarity : 0.004 0.059 2931 Dihedral : 28.220 165.546 5295 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.77 % Allowed : 17.76 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1825 helix: 1.36 (0.17), residues: 1045 sheet: -1.91 (0.45), residues: 125 loop : -1.67 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 267 HIS 0.005 0.001 HIS N 402 PHE 0.028 0.002 PHE N 122 TYR 0.022 0.001 TYR N 499 ARG 0.014 0.000 ARG N 645 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 1073) hydrogen bonds : angle 3.64487 ( 2808) covalent geometry : bond 0.00316 (22116) covalent geometry : angle 0.62737 (31129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8840 (tm) REVERT: A 94 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8476 (mm-30) REVERT: C 90 ASP cc_start: 0.8534 (t0) cc_final: 0.8323 (t0) REVERT: D 90 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8277 (pm20) REVERT: D 105 LYS cc_start: 0.8718 (mtpm) cc_final: 0.8511 (mttp) REVERT: E 68 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: E 73 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8662 (tm-30) REVERT: E 106 ASP cc_start: 0.8297 (m-30) cc_final: 0.7992 (m-30) REVERT: F 93 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: G 104 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8692 (mm110) REVERT: H 90 GLU cc_start: 0.8871 (mp0) cc_final: 0.8477 (mp0) REVERT: K 525 SER cc_start: 0.8908 (m) cc_final: 0.8414 (t) REVERT: K 722 LEU cc_start: 0.7898 (mm) cc_final: 0.7656 (mm) REVERT: N 527 MET cc_start: 0.8227 (mtp) cc_final: 0.7621 (ttm) REVERT: N 645 ARG cc_start: 0.9015 (ttp80) cc_final: 0.8724 (tmm-80) outliers start: 45 outliers final: 15 residues processed: 222 average time/residue: 1.3230 time to fit residues: 335.4099 Evaluate side-chains 180 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 424 LYS Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 335 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 0.0370 chunk 92 optimal weight: 3.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.093140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.065919 restraints weight = 62086.140| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.69 r_work: 0.3058 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 22116 Z= 0.203 Angle : 0.654 13.582 31129 Z= 0.351 Chirality : 0.039 0.180 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.298 165.972 5295 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.64 % Allowed : 19.48 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1825 helix: 1.30 (0.17), residues: 1050 sheet: -2.20 (0.44), residues: 126 loop : -1.62 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP K 384 HIS 0.005 0.001 HIS K 121 PHE 0.025 0.002 PHE N 122 TYR 0.019 0.001 TYR N 199 ARG 0.008 0.000 ARG N 645 Details of bonding type rmsd hydrogen bonds : bond 0.05171 ( 1073) hydrogen bonds : angle 3.71023 ( 2808) covalent geometry : bond 0.00461 (22116) covalent geometry : angle 0.65361 (31129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 1.999 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8862 (tm) REVERT: A 94 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8568 (mm-30) REVERT: C 90 ASP cc_start: 0.8620 (t0) cc_final: 0.8343 (t0) REVERT: D 90 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: D 105 LYS cc_start: 0.8866 (mtpm) cc_final: 0.8654 (mttp) REVERT: E 68 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: E 73 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 106 ASP cc_start: 0.8347 (m-30) cc_final: 0.8004 (m-30) REVERT: E 120 MET cc_start: 0.8175 (mtt) cc_final: 0.7857 (mtt) REVERT: F 93 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: G 91 GLU cc_start: 0.8345 (pm20) cc_final: 0.7617 (pm20) REVERT: G 92 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8593 (mp0) REVERT: G 104 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8696 (mm110) REVERT: H 90 GLU cc_start: 0.8924 (mp0) cc_final: 0.8482 (mp0) REVERT: K 279 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7375 (p0) REVERT: K 609 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8119 (pp-130) REVERT: K 722 LEU cc_start: 0.7922 (mm) cc_final: 0.7690 (mm) REVERT: N 527 MET cc_start: 0.8235 (mtp) cc_final: 0.7637 (ttm) outliers start: 43 outliers final: 20 residues processed: 196 average time/residue: 1.4318 time to fit residues: 316.6207 Evaluate side-chains 182 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 279 ASP Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 609 MET Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 371 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN H 46 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066729 restraints weight = 62397.825| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.70 r_work: 0.3087 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22116 Z= 0.159 Angle : 0.638 13.984 31129 Z= 0.342 Chirality : 0.038 0.221 3509 Planarity : 0.004 0.061 2931 Dihedral : 28.224 166.696 5295 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.03 % Allowed : 20.41 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1825 helix: 1.33 (0.17), residues: 1060 sheet: -2.32 (0.42), residues: 131 loop : -1.52 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP K 384 HIS 0.004 0.001 HIS K 402 PHE 0.026 0.002 PHE N 122 TYR 0.019 0.001 TYR N 499 ARG 0.014 0.000 ARG N 645 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1073) hydrogen bonds : angle 3.61633 ( 2808) covalent geometry : bond 0.00357 (22116) covalent geometry : angle 0.63785 (31129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 170 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8877 (tm) REVERT: A 94 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8508 (mm-30) REVERT: C 90 ASP cc_start: 0.8516 (t0) cc_final: 0.8282 (t0) REVERT: D 90 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: E 68 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: E 73 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8666 (tm-30) REVERT: E 106 ASP cc_start: 0.8251 (m-30) cc_final: 0.7935 (m-30) REVERT: E 120 MET cc_start: 0.8094 (mtt) cc_final: 0.7807 (mtt) REVERT: F 93 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: G 36 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8788 (mmpt) REVERT: G 91 GLU cc_start: 0.8237 (pm20) cc_final: 0.7637 (pm20) REVERT: G 104 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8728 (mm110) REVERT: H 90 GLU cc_start: 0.8908 (mp0) cc_final: 0.8530 (mp0) REVERT: K 123 ILE cc_start: 0.7421 (mp) cc_final: 0.7168 (mp) REVERT: K 525 SER cc_start: 0.9001 (m) cc_final: 0.8399 (t) REVERT: K 722 LEU cc_start: 0.7923 (mm) cc_final: 0.7686 (mm) REVERT: N 527 MET cc_start: 0.8324 (mtp) cc_final: 0.7698 (ttm) REVERT: N 606 LEU cc_start: 0.8803 (tt) cc_final: 0.8521 (mt) outliers start: 33 outliers final: 17 residues processed: 192 average time/residue: 1.4741 time to fit residues: 320.3276 Evaluate side-chains 179 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 230 GLN Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 7 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN E 85 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.092297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.064985 restraints weight = 62337.591| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.68 r_work: 0.3038 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 22116 Z= 0.266 Angle : 0.693 14.395 31129 Z= 0.370 Chirality : 0.041 0.296 3509 Planarity : 0.004 0.052 2931 Dihedral : 28.347 167.050 5295 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.21 % Allowed : 21.20 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.21), residues: 1825 helix: 1.26 (0.17), residues: 1044 sheet: -2.18 (0.44), residues: 126 loop : -1.65 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 384 HIS 0.006 0.001 HIS B 75 PHE 0.025 0.002 PHE N 122 TYR 0.021 0.002 TYR N 499 ARG 0.009 0.001 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.05575 ( 1073) hydrogen bonds : angle 3.75042 ( 2808) covalent geometry : bond 0.00609 (22116) covalent geometry : angle 0.69312 (31129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8913 (tm) REVERT: A 94 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8552 (mm-30) REVERT: C 90 ASP cc_start: 0.8621 (t0) cc_final: 0.8383 (t0) REVERT: E 68 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: E 73 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8697 (tm-30) REVERT: E 106 ASP cc_start: 0.8334 (m-30) cc_final: 0.8027 (m-30) REVERT: E 120 MET cc_start: 0.8271 (mtt) cc_final: 0.7970 (mtt) REVERT: F 93 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: G 36 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8897 (mmpt) REVERT: G 64 GLU cc_start: 0.8822 (tt0) cc_final: 0.8370 (tm-30) REVERT: G 104 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8741 (mm110) REVERT: H 90 GLU cc_start: 0.8902 (mp0) cc_final: 0.8503 (mp0) REVERT: K 722 LEU cc_start: 0.8024 (mm) cc_final: 0.7778 (mm) REVERT: N 527 MET cc_start: 0.8219 (mtp) cc_final: 0.7684 (ttm) REVERT: N 606 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8544 (mt) outliers start: 36 outliers final: 21 residues processed: 180 average time/residue: 1.5786 time to fit residues: 326.9000 Evaluate side-chains 177 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain K residue 546 CYS Chi-restraints excluded: chain N residue 122 PHE Chi-restraints excluded: chain N residue 298 VAL Chi-restraints excluded: chain N residue 606 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 133 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN E 85 GLN ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.093741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066712 restraints weight = 62387.116| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.71 r_work: 0.3081 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22116 Z= 0.160 Angle : 0.650 12.376 31129 Z= 0.347 Chirality : 0.038 0.342 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.234 167.636 5295 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.54 % Allowed : 22.00 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.21), residues: 1825 helix: 1.39 (0.17), residues: 1048 sheet: -2.12 (0.47), residues: 116 loop : -1.50 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 384 HIS 0.004 0.001 HIS K 111 PHE 0.028 0.002 PHE N 122 TYR 0.022 0.001 TYR N 499 ARG 0.006 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 1073) hydrogen bonds : angle 3.58998 ( 2808) covalent geometry : bond 0.00358 (22116) covalent geometry : angle 0.64988 (31129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9022 (pm20) cc_final: 0.8619 (pm20) REVERT: A 65 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8785 (tm) REVERT: A 94 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8543 (mm-30) REVERT: C 90 ASP cc_start: 0.8513 (t0) cc_final: 0.8256 (t0) REVERT: E 59 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7983 (pm20) REVERT: E 68 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: E 106 ASP cc_start: 0.8354 (m-30) cc_final: 0.8031 (m-30) REVERT: E 120 MET cc_start: 0.8102 (mtt) cc_final: 0.7767 (mtt) REVERT: F 93 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: G 36 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8873 (mmpt) REVERT: G 104 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8716 (mm110) REVERT: H 90 GLU cc_start: 0.8966 (mp0) cc_final: 0.8478 (mp0) REVERT: K 108 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8281 (ptp-110) REVERT: K 279 ASP cc_start: 0.7997 (p0) cc_final: 0.7587 (p0) REVERT: K 722 LEU cc_start: 0.7985 (mm) cc_final: 0.7760 (mm) REVERT: N 527 MET cc_start: 0.8289 (mtp) cc_final: 0.7685 (ttm) REVERT: N 606 LEU cc_start: 0.8660 (tt) cc_final: 0.8447 (mt) outliers start: 25 outliers final: 14 residues processed: 192 average time/residue: 1.5175 time to fit residues: 328.0660 Evaluate side-chains 179 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 153 optimal weight: 0.5980 chunk 206 optimal weight: 3.9990 chunk 127 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN K 121 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.094646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067785 restraints weight = 62388.327| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.73 r_work: 0.3100 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22116 Z= 0.150 Angle : 0.650 12.914 31129 Z= 0.346 Chirality : 0.038 0.322 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.089 167.246 5295 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.29 % Allowed : 22.37 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1825 helix: 1.48 (0.17), residues: 1038 sheet: -2.06 (0.47), residues: 114 loop : -1.50 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 260 HIS 0.017 0.001 HIS K 121 PHE 0.026 0.002 PHE K 122 TYR 0.025 0.001 TYR N 499 ARG 0.009 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04661 ( 1073) hydrogen bonds : angle 3.51526 ( 2808) covalent geometry : bond 0.00333 (22116) covalent geometry : angle 0.65039 (31129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9022 (pm20) cc_final: 0.8675 (pm20) REVERT: A 65 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8769 (tm) REVERT: A 94 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8545 (mm-30) REVERT: C 90 ASP cc_start: 0.8479 (t0) cc_final: 0.8210 (t0) REVERT: E 59 GLU cc_start: 0.8407 (pm20) cc_final: 0.7875 (pm20) REVERT: E 68 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: E 106 ASP cc_start: 0.8368 (m-30) cc_final: 0.8028 (m-30) REVERT: E 120 MET cc_start: 0.8054 (mtt) cc_final: 0.7726 (mtt) REVERT: F 93 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: G 36 LYS cc_start: 0.9133 (mmtm) cc_final: 0.8876 (mmpt) REVERT: G 104 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8751 (mm110) REVERT: H 90 GLU cc_start: 0.8964 (mp0) cc_final: 0.8483 (mp0) REVERT: K 108 ARG cc_start: 0.8969 (mtm-85) cc_final: 0.8342 (ptp-110) REVERT: K 210 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8541 (mm) REVERT: K 279 ASP cc_start: 0.7986 (p0) cc_final: 0.7481 (p0) REVERT: K 426 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7473 (pm20) REVERT: K 525 SER cc_start: 0.9040 (m) cc_final: 0.8390 (t) REVERT: K 722 LEU cc_start: 0.7960 (mm) cc_final: 0.7733 (mm) REVERT: N 205 ASN cc_start: 0.9042 (m-40) cc_final: 0.8664 (p0) REVERT: N 221 ASP cc_start: 0.5639 (m-30) cc_final: 0.5218 (m-30) REVERT: N 527 MET cc_start: 0.8282 (mtp) cc_final: 0.7750 (ttm) outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 1.3793 time to fit residues: 305.0758 Evaluate side-chains 182 residues out of total 1637 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 406 GLN Chi-restraints excluded: chain K residue 533 ILE Chi-restraints excluded: chain N residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 117 optimal weight: 0.7980 chunk 121 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 68 optimal weight: 0.0870 chunk 133 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 24 GLN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** K 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.095275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068432 restraints weight = 62950.369| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.76 r_work: 0.3118 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22116 Z= 0.144 Angle : 0.642 13.995 31129 Z= 0.342 Chirality : 0.038 0.302 3509 Planarity : 0.004 0.053 2931 Dihedral : 28.006 167.608 5295 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.35 % Allowed : 22.62 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1825 helix: 1.48 (0.17), residues: 1046 sheet: -2.01 (0.46), residues: 119 loop : -1.45 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 384 HIS 0.014 0.001 HIS K 361 PHE 0.029 0.002 PHE N 122 TYR 0.033 0.001 TYR N 499 ARG 0.008 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.04536 ( 1073) hydrogen bonds : angle 3.46833 ( 2808) covalent geometry : bond 0.00320 (22116) covalent geometry : angle 0.64154 (31129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13644.67 seconds wall clock time: 232 minutes 54.58 seconds (13974.58 seconds total)